


Surprise After Surprise

by afteriwake



Series: And Now I'm Learning You [23]
Category: Doctor Who, Sherlock (TV), Star Trek: Alternate Original Series (Movies)
Genre: F/M, Gen
Language: English
Status: Completed
Published: 2014-10-17
Updated: 2014-10-17
Packaged: 2018-02-21 11:41:28
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,838
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2466947
Author URL: https://archiveofourown.org/users/afteriwake/pseuds/afteriwake
Summary: <blockquote class="userstuff">
              <p>Molly comes home after learning some surprising news to find Mycroft at her home. When she insists there be no secrets between the five of them who are all directly affected by Khan pretending to be Sherlock’s twin brother she gets even more surprising news about exactly what the Doctor and Sherlock have found out in regards to Khan and Carlton being clones.</p>
            </blockquote>





	Surprise After Surprise

**Author's Note:**

> So. Yes. I love big twists.

Molly let herself into her home, doing so quietly. It was only one in the afternoon and it had already been a long day with some surprising news. She set her handbag on the table in the foyer. “Are you home, Khan?” she called out.

“We have company,” she heard him say sullenly from the sitting room.

“Lovely,” she said under her breath. She squared her shoulders and made her way to the sitting room, not at all surprised to see Mycroft there. “Hello, Mycroft.”

He inclined his head towards her. “Molly.”

“Any particular reason you decided to pay us a visit?” she asked, moving over to the sofa to sit next to Khan.

“My brother is keeping secrets,” he said. “And my parents suddenly want nothing to do with either of you. Khan won't tell me why, either.”

“Is it really all that important?” Khan asked. “The mess you got all of us into got solved. Just let it go.”

Mycroft turned to Molly. “I don't like being kept in the dark.”

“Maybe the Doctor should explain,” she said with a sigh.

Mycroft leaned back into the seat. “It has something to do with the two of you, doesn't it?”

Khan shook his head. “Just me.”

“I swear, this entire affair has turned into a rather large headache,” Mycroft said, running a hand down his face.

Molly was quiet for a moment, then she stood up. Both men turned to her but she ignored them and went to her handbag. She got out her mobile phone and then went back to the sitting room. After a moment she pulled up a contact and hit send before putting the phone on speaker. It rang three times before Sherlock answered. “Molly?”

“Are you still with the Doctor?” she asked.

“I was just about to leave the TARDIS,” he said.

“Put your phone on speaker and have him listen. I want all four of you to hear what I have to say.”

“Four?” Sherlock asked.

“Khan and Mycroft are currently in my sitting room.”

“I'm sorry,” he said.

“Well, move over towards him so I can get this over and done with once and for all,” she said.

There was a pause, and then the Doctor spoke. “Molly? Is something wrong?”

“No, but it could be and I don't want it to be. I don't want any secrets being kept from _any_ of us who are involved in all of this. I don't care about personal feelings towards each other, I don't care about sibling rivalry, any of that. I have had a long day and I’m stressed and I want to relax. So all five of us are going to talk about what's been happening, and the five of us are going to continue to all talk to each other as we figure out what the bloody hell is going on. Understood?” She heard murmurs of agreement from Sherlock and the Doctor, and then she looked over at Mycroft and Khan, who both nodded. “Doctor, you start.”

“Very well. You were not told the entire truth about how we ended the threat Moriarty posed, Mycroft. He used a flesh duplicate to fool Sherlock on the roof the first time. The stain in the bottom of the coffin was from the Ganger.”

“So how did you stop him?” Mycroft asked.

“There is a crew of people who inhabit a robot that take care of the most notorious criminals in the galaxy, the ones who escape punishment. The robot they use is called the Tesselecta. I assume Kate has told you I had faked my death a few years back?”

“Yes,” Mycroft said with a nod. “It was a fixed point in time, I believe.”

“Yes, it was. The crew allowed me to use the robot to convince those who were plotting against me that I was dead. It didn't last for long, but it did take care of making sure events happened as they should.”

“Why is this important?” Mycroft asked, beginning to sound annoyed.

“Because the Doctor had them take the real Moriarty out of the picture that way, you--” Sherlock began irritatedly.

“Sherlock?” Molly said, cutting him off.

“Yes?”

“Don't start.”

“But he--”

“ _Don't,_ ” she said, sounding slightly annoyed. Sherlock remained silent. “When the threat was gone, Khan and I stayed on board with the Doctor. That much you know. But Sherlock, Khan and the Doctor would talk when all of them were on board. The question of how Moriarty got a Ganger was a frequent topic of conversation, from what I was told.”

“Yes,” the Doctor said. “Moriarty liked to brag. He had fully expected to see Sherlock and I on the roof. Well, Khan as well, even though it wasn't _really_ Khan. Anyway, he said that he'd moved on to bigger things, better things. He was starting to tire of Earth, he said, and had been trying to move farther afield. But then he said he'd ignored Earth too long and the people who gave him his golden opportunity to become the biggest crime lord in the universe told him to fix the problem. They told him the truth about Khan and my involvement in matters. That was why he left the note he did. I wanted to find out more but he attempted to kill Sherlock. The crew of the Tesselecta collected him at that point.”

“Neither of you told us that,” Molly said, her eyes wide.

“I knew,” Khan said quietly. She glared at him. “Only after the fact, though. And it was decided it would be best if you didn't have a need to worry.”

“I am simply fascinated by how the three of you decided for me what I should or shouldn't know,” she said coldly.

“Don't be upset with Khan and Sherlock, Molly,” the Doctor said hurriedly. “They both wanted to tell you. I insisted they didn't. You'd been through enough at that point, and he was gone. He wasn't ever going to hurt you again.”

She shut her eyes. “We'll deal with that later, I suppose.”

“The point Molly was trying to make was, the three of us talked and discussed things and got more information,” Sherlock said. “But it wasn't until you put your foot in your mouth and told Mum and Dad about Khan and Molly's engagement that we learned something of importance.”

“What did you learn?” Mycroft asked.

“Khan and Carlton are clones,” the Doctor said. “And I had planned on telling both Molly and Khan today, but we know who they are a clone of now.”

“Who was it?” Khan asked.

“Me,” Sherlock said quietly.

Molly's jaw was hanging slightly and both Khan and Mycroft looked shocked. “Go back a moment,” Mycroft said when he collected himself. “How did all of this come up?”

“You wanted Khan to have Carlton's memories so he could fool our parents. But I had discovered something about Carlton before your gaffe,” Sherlock said. “Carlton wasn't schizophrenic. Someone who knew him when he was homeless, before he was murdered, recounted to me in exact detail the ramblings that Carlton used to have. Quite a few instances matched up nearly word for word of things Khan had told me about his time in his universe.”

“But he's from an alternate universe,” Mycroft said.

“Apparently it didn't matter. They were linked because they were clones,” the Doctor said. “I suspect the reason Khan doesn't have the memories of Carlton's life in his head was because when Khan's memory was modified it changed his brain. The link between the two of them was there, but it was dormant. Carlton only seems to have remembered things before Khan was cryogenically frozen, so it must only have been what they went through when they were alive at approximately the same time. Carlton is dead now, though, so I suppose we'll never know for sure.”

“How did you figure out they were cloned from Sherlock, though?” Molly asked.

“The last time I met Sherlock and Mycroft's parents, my only intent had been to implant the suggestion that they want nothing to do with Carlton Holmes. But Khan called me three days ago with what the two of you had discussed. I didn't realize he had seen their mother's face when I pulled up his memories of his encounter. So I decided to get Sherlock and pay them another visit.”

“Mycroft, Mum knew,” Sherlock said. “When she was pregnant with me someone who said they represented the Great Intelligence promised her she would be quite important if she let them take a DNA sample from me in utero. They would give her another child to raise and she would do great things in furtherance of their goals. And she let them.”

“Someone had perfected the art of traveling between universes, and traveling through time as well,” the Doctor said. “They came from Khan's universe to this one to collect the samples. A few weeks after Sherlock was born they came back with two infants, Carlton and Khan. There was an argument and she insisted she would only take one. Carlton had been considered a nonviable clone so he was allowed to stay and Khan was sent back. But in retaliation for not going along with the plan your mother's memories were modified as well.”

“So in a way I actually am your brother,” Khan said quietly, leaning back into his seat. “But why Sherlock?”

“We don't know yet,” the Doctor said. “We still have more questions than we have answers. Sherlock and I spent the day tracking down the doctor who delivered Sherlock and the hospital staff. We made an interesting discovery.”

“The vast majority of the staff at the hospital have died, either by accident or by taking their own lives,” Sherlock said. “Many had strange memories surface, remembered events that night two different ways. We managed to track down the doctor who delivered me, but he's old and in a home for the elderly. But we got to see clearly his memories of the night I was delivered, before his memories were modified. There was someone else in the delivery room that Mum insisted be there. A man in a hooded cloak. He made the staff uneasy, but the doctor we visited managed to get a glimpse of what was under the hood.”

“I'm attempting to figure it all out now,” the Doctor said. “But I was able to project the image I saw onto psychic paper. Sherlock said he'd seen him before.”

“Mycroft, do you remember when Carlton and I were ten, and we were fighting over the last Cadbury crème on Christmas morning, and I stormed out of the house when Mum gave it to him?” Sherlock asked.

“I do,” Mycroft said with a slow nod. “You said there was a strange man standing outside the window, and Mother and Father didn't believe you. You were quite insistent”

“The man I saw that day and the man in the delivery room were the same man,” Sherlock said. “Exactly the same. He hadn't aged a day. And I saw him one other time, the day after Carlton left. He purposefully bumped into me as I left our home that morning to get away from Mum's histrionics. He still looked the same.”

Mycroft leaned forward. “So this man has been keeping an eye on Carlton?” he said slowly.

“It appears so,” the Doctor said. “I was going to go to the day Carlton was murdered to check out a hunch. Sherlock declined to accompany me.”

“You think this man was involved in his murder,” Khan said.

“Yes, I do,” the Doctor said quietly. “Carlton was a loose end at that point. And he was talking about things he shouldn't.”

“Is he still around?” Molly asked worriedly.

“We don't know,” Sherlock said. “But if it helps ease your mind, I haven't seen him again since I was sixteen.”

“I want to see what he looks like,” Khan said. “I have an eidetic memory. If I've seen him I'll know as soon as I look at that photo.”

“I'll show you as soon as I can,” the Doctor said. “But that is everything we know now.”

“I will see what I can do to assist all of you,” Mycroft said. “I'm quite curious as to what exactly has been going on for the last thirty-three years.”

“You and I both,” Sherlock said. “Do Mum and Dad still want to associate with you? Because I told her I'd choose Carlton over them any day and I was disowned on the spot.”

“I've simply ignored their requests to speak with me,” Mycroft said. “It might not be a bad idea to not alienate them, though. I can always pretend I'm not remotely interested in what my dear brothers are doing even if it's not the truth.”

“Is it going to stick, though?” Molly asked.

“I've been pretending I hate Sherlock for the last sixteen years, and done a very good job convincing my parents and the world at large of that fact,” Mycroft said, standing up and straightening his suit jacket. “I'm sure I can convince them Carlton is of no importance to me.”

“It's actually heartening to know you care,” Sherlock said quietly.

“While our parents have done quite a few things to garner my resentment the only thing you have done is occasionally be an annoying thorn in my side at inopportune times,” Mycroft said. “And from what I'm told that is a baby brother's prerogative. As it stands, I will play my part in this and pay attention to what they say, and alert you if anything changes.”

“You might as well have a way to meet with me directly,” the Doctor said. “Do you have plans this afternoon?”

“Nothing I can't put off for a time,” Mycroft said.

“I can drop Sherlock off at your home, Molly, and pick Mycroft up.”

Molly sighed. "You aren't going to be staying long, Sherlock, are you?”

“I wasn't going to stay at all,” Sherlock said. “I have a case I need to get back to. I only took time away to help the Doctor for my own curiosity.”

“I'll take you out the back,” Khan said, standing up. “And make sure you have that picture to show me, Doctor.”

“I will. I'll speak to you later, Molly,” the Doctor said.

“All right,” she said. She hung up the phone and looked up at Mycroft. “So now you know everything we know.”

“It is quite troubling,” he said quietly. Then he turned to Khan. “Even though you are a clone, I will begin to actually consider you my brother. I'm assuming you have the same genetic make-up that Sherlock and I do, and that makes you actual family in my eyes.”

Khan nodded slowly. “I suppose I should do the same for you,” he replied. Then he gestured towards the back hallway. “The Doctor's probably waiting.”

“Very well,” Mycroft said. He picked up his umbrella, which had been leaning against the chair he had been sitting in.

“I'll be back soon,” Khan said to Molly, who simply nodded in response. Then he and Mycroft left, and Molly got up to go into the kitchen. She was nervous, and as the minutes ticked by the nervousness grew. Finally, six minutes later, she heard the door opening again and Khan came out. “I haven't seen that man here,” he said.

She was relieved and was about to say something when she paused. “But you have seen him?” she asked quietly.

He nodded slowly. “He was in charge of the program that made us. Henry Guillen was his name. What took so long was I mentioned a possibility to the Doctor that he should look into.”

“What possibility was that?” she asked.

He leaned against the counter. “That every single person I was in that program with was a clone, and Guillen traveled to this universe to get the samples to clone them from.”

Her eyes widened. “How many of you were in that program?”

“There were at least a thousand of us. It may have been more widespread than that. But by the time the Eugenics War was over our weaknesses had been found out an exploited. My crew and I were all that remained of that program. There are about five dozen of us left, and of them I am, as far as I know, the only one actually walking around.”

“So what is the Doctor going to do?” she asked.

“He's going to see if there is a way to travel back to my home universe,” he said quietly. “He wants answers and that's the only place to get them.”

“Are you going with him?” she asked quietly.

“No. There's too much risk that I'll be forced to stay,” he said. “Sherlock won't be going, either, because of the resemblance.” He pulled away from the counter and moved over towards her. When he got close he reached over to gently touch her face. “I won't leave you, not even to get answers. I want to start a life here with you in this time and place. That's more important to me than this mystery the Doctor is trying to unravel.”

She nodded. “I'm glad. Because there's something you need to know.”

“What is it?” he asked.

She moved away from him slightly and began to pace. “The whole time we've been together, I've...I mean even before we were I was on it and I'm usually very good at making sure I get the shot on time and I missed and we haven't even _talked_ about this, not really, and I don't want you to be upset.”

He watched her get that all out before moving in her path and putting his hands on her shoulders. “Molly, what happened?”

“I'm pregnant,” she said quietly, looking down. “I've been feeling nauseated in the mornings and because I had been on birth control I thought it was just stress with all of this but last night I realized I should have had my shot two months ago, so I went to my doctor this morning and she did a pregnancy test. I'm seven weeks pregnant.”

He looked at her with wide eyes. “I didn't even think that was possible,” he said quietly. “We had been told we were sterilized.”

“Well, you weren't,” she said. “I haven't been with anyone but you since the first night we were together.”

“I don't doubt that,” he said, moving his hand to tilt her face up. “I just never entertained it as a possibility. I've never even thought if I wanted to be a father. Did you want to have children?”

“I do,” she said. “I just wasn't expecting them now, or expecting to be pregnant at all, really. But I do want at least one child. Do you want children?”

“I don't know,” he said quietly. She turned her body away from him. “Molly, this is a shock. You have to let me come to grips with it.”

“I'm keeping the baby,” she said adamantly. “Whether you end up staying or not, I'm keeping the baby. If you decide to leave we can split the money in the account so you'll be taken care of and I'm sure Mycroft can help you out as well. But I want this child and if I have to raise it on my own so be it.”

“Why are you planning that I won't stay?” he asked, beginning to get angry. “I chose you over the people I had sworn to protect. It's not as though I think you did this on purpose. And I'll admit I think I'll make a terrible father but once I get used to the idea I'll be more willing to try. But you have to let me get used to the idea, all right?”

She shook her head. “I just...I can't be here. I can't do this right now.” 

“Molly,” he called out, but she ignored him. She left the kitchen and made her way to the foyer to get her handbag. She made it there and grabbed it, looking through it for a moment before realizing her phone was in the sitting room. She went back there and got it off the sofa, shoving it into her handbag. This had gone just as badly as she had expected, she knew that. She glanced in the kitchen and saw Khan facing the sink, both hands on the counter and head bowed. That was all she gave him, though, before she went back to the front door and let herself out. She didn't have a place in mind to go. She just knew she couldn't be near Khan right now. She could go to Amy's and see if she was home but she didn't really want to do that. When she told her friend the good news she didn't want uncertainty attached to it. She wanted to know whether he'd stay or whether she'd be doing it on her own.

She wandered around for three hours, more or less moving aimlessly. Finally she just didn't want to walk anymore and so she caught a cab back to her home. She let herself in and saw the sitting room and kitchen were empty. The only thing that was different was the note set on the island in the kitchen. She picked it up and opened it. _I want a girl_ was all it said, and she felt a smile form on her face, growing wider by the minute. She set the note down and looked around. “Khan?” she called out loudly

There wasn't an answer at first, but soon she heard footsteps coming down the stairs. “You read the note?” he asked when he came into the kitchen.

“You're going to stay?” she asked, moving towards him.

“You'll have to help me not be a horrible father,” he said as he nodded. “You'll have to be patient with me when I do the wrong thing. And you have to promise that when I do something right you tell me so I can learn what I'm supposed to do.”

“I can do that. I can do all of that,” she said, getting close enough to wrap her arms around his neck. She stood up on her toes and leaned in the kiss him. He pulled her close and then deepened the kiss. When they finally pulled apart she looked up at him, a wide smile on her face. “I'll make sure you're a great dad.”

“Good,” he said with a nod. 

She moved slightly and put her arms around his waist, hugging him, and he embraced her back. This was good. No, this was excellent. He was happy with the news and he was going to stay. She could let go of the worry and be happy, knowing he was happy too. It was quite unexpected, but maybe it as a good thing after all.


End file.
